Antifungal resistance is increasing by the emergence of intrinsically resistant species and by the development of secondary resistance in susceptible species. A previous study performed in Spain revealed levels of azole resistance in molds between 10 to 12.7% but secondary resistance in A. fumigatus was not detected. We used itraconazole supplemented media to select resistant strains. A total of 500 plates supplemented with 2 mg/L of ITZ were sent to 10 Spanish tertiary hospitals, molecular identification and antifungal susceptibility testing were performed. In addition, cyp51A gene was sequenced in those A. fumigatus strains showing azole resistance. A total of 493 isolates were included in the study. Sixteen strains were isolated from patients with an infection classified as proven, 104 as probable and 373 as colonization. Aspergillus was the most frequent genera isolated with 80.3% followed by Scedosporium/Lomentospora (7.9%), Penicillium/Talaromyces (4.5%), Fusarium (2.6 %) and the order Mucorales (1 %). Antifungal resistance was detected in Scedosporium/Lomentospora species, Fusarium, Talaromyces and Mucorales. Three strains of A. fumigatus senso stricto were resistant to azoles, two of them harbored TR34+L98H mechanism of resistance and the other one had no mutations in cyp51A. The level of azole resistance in A. fumigatus remains low but cryptic species represent over 10% of the isolates and have broader but overall higher range of antifungal resistance.